Youyi Kuang

QTL variations for growth-related traits in eight distinct families of common carp (Cyprinus carpio).

BackgroundComparing QTL analyses of multiple pair-mating families can provide a better understanding of important allelic variations and distributions. However, most QTL mapping studies in common carp have been based on analyses of individual families. In order to improve our understanding of heredity and variation of QTLs in different families and identify important QTLs, we performed QTL analysis of growth-related traits in multiple segregating families.ResultsWe completed a genome scan for QTLs that affect body weight (BW), total length (TL), and body thickness (BT) of 522 individuals from eight full-sib families using 250 microsatellites evenly distributed across 50 chromosomes. Sib-pair and half-sib model mapping identified 165 QTLs on 30 linkage groups. Among them, 10 (genome-wide P <0.01 or P < 0.05) and 28 (chromosome-wide P < 0.01) QTLs exhibited significant evidence of linkage, while the remaining 127 exhibited a suggestive effect on the above three traits at a chromosome-wide (P < 0.05) level. Multiple QTLs obtained from different families affect BW, TL, and BT and locate at close or identical positions. It suggests that same genetic factors may control variability in these traits. Furthermore, the results of the comparative QTL analysis of multiple families showed that one QTL was common in four of the eight families, nine QTLs were detected in three of the eight families, and 26 QTLs were found common to two of the eight families. These common QTLs are valuable candidates in marker-assisted selection.ConclusionA large number of QTLs were detected in the common carp genome and associated with growth-related traits. Some of the QTLs of different growth-related traits were identified at similar chromosomal regions, suggesting a role for pleiotropy and/or tight linkage and demonstrating a common genetic basis of growth trait variations. The results have set up an example for comparing QTLs in common carp and provided insights into variations in the identified QTLs affecting body growth. Discovery of these common QTLs between families and growth-related traits represents an important step towards understanding of quantitative genetic variation in common carp.

The genetic map of goldfish ( Carassius auratus ) provided insights to the divergent genome evolutions in the Cyprinidae family

A high-density linkage map of goldfish (Carassius auratus) was constructed using RNA-sequencing. This map consists of 50 linkage groups with 8,521 SNP markers and an average resolution of 0.62 cM. Approximately 84% of markers are in protein-coding genes orthologous to zebrafish proteins. We performed comparative genome analysis between zebrafish and medaka, common carp, grass carp, and goldfish to study the genome evolution events in the Cyprinidae family. The comparison revealed large synteny blocks among Cyprinidae fish and we hypothesized that the Cyprinidae ancestor undergone many inter-chromosome rearrangements after speciation from teleost ancestor. The study also showed that goldfish genome had one more round of whole genome duplication (WGD) than zebrafish. Our results illustrated that most goldfish markers were orthologous to genes in common carp, which had four rounds of WGD. Growth-related regions and genes were identified by QTL analysis and association study. Function annotations of the associated genes suggested that they might regulate development and growth in goldfish. This first genetic map enables us to study the goldfish genome evolution and provides an important resource for selective breeding of goldfish.

The Transcriptomes of the Crucian Carp Complex (Carassius auratus) Provide Insights into the Distinction between Unisexual Triploids and Sexual Diploids

Both sexual reproduction and unisexual reproduction are adaptive strategies for species survival and evolution. Unisexual animals have originated largely by hybridization, which tends to elevate their heterozygosity. However, the extent of genetic diversity resulting from hybridization and the genomic differences that determine the type of reproduction are poorly understood. In Carassius auratus, sexual diploids and unisexual triploids coexist. These two forms are similar morphologically but differ markedly in their modes of reproduction. Investigation of their genomic differences will be useful to study genome diversity and the development of reproductive mode. We generated transcriptomes for the unisexual and sexual populations. Genes were identified using homology searches and an ab initio method. Estimation of the synonymous substitution rate in the orthologous pairs indicated that the hybridization of gibel carp occurred 2.2 million years ago. Microsatellite genotyping in each individual from the gibel carp population indicated that most gibel carp genes were not tri-allelic. Molecular function and pathway comparisons suggested few gene expansions between them, except for the progesterone-mediated oocyte maturation pathway, which is enriched in gibel carp. Differential expression analysis identified highly expressed genes in gibel carp. The transcriptomes provide information on genetic diversity and genomic differences, which should assist future studies in functional genomics.

Duplication and differentiation of common carp (Cyprinus carpio) myoglobin genes revealed by BAC analysis

Two distinct myoglobin (mb) transcripts have been reported in common carp, Cyprinus carpio, which is a hypoxia-tolerant fish living in habitats with greatly fluctuant dissolved oxygen levels. Recombinant protein analysis has shown functional specialization of the two mb transcripts. In this work, analysis for mb-containing bacterial artificial chromosome (BAC) clones indicated different genome loci for common carp myoglobin-1 (mb-1) and myoglobin-2 (mb-2) genes. Fluorescence in situ hybridization (FISH) revealed that mb-1 and mb-2 are located on separate chromosomes. In both of the mb-1 and mb-2 containing BAC clones, gene synteny was well conserved with the homologous region on zebrafish chromosome 1, supporting that the common carp specific mb-2 gene originated from the recent whole genome duplication event in cyprinid lineage. Transcription factor binding sites search indicated that both common carp mb genes lacked specificity Protein 1 (Sp1) and myocyte enhancer factor-2 (MEF2) binding sites, which mediated muscle-specific and calcium-dependent expression in the well-studied mb promoters. Potential hypoxia response elements (HREs) were predicted in the regulatory region of common carp mb genes. These characteristics of common carp mb gene regulatory region well interpreted the hypoxia-inducible, non-muscle expression pattern of mb-1. In the case of mb-2, a 10 bp insertion to the binding site of upstream stimulatory factor (USF), which was a co-factor of hypoxia inducible factor (HIF), might cause the non-response to hypoxia treatment of mb-2. The case of common carp mb gene duplication and subsequent differentiation in expression pattern and protein function provided an example for adaptive evolution toward aquatic hypoxia tolerance.

Genome-Wide Association Study for Muscle Fat Content and Abdominal Fat Traits in Common Carp (Cyprinus carpio)

Muscle fat content is an important phenotypic trait in fish, as it affects the nutritional, technical and sensory qualities of flesh. To identify loci and candidate genes associated with muscle fat content and abdominal fat traits, we performed a genome-wide association study (GWAS) using the common carp 250 K SNP assay in a common carp F2 resource population. A total of 18 loci surpassing the genome-wide suggestive significance level were detected for 4 traits: fat content in dorsal muscle (MFdo), fat content in abdominal muscle (MFab), abdominal fat weight (AbFW), and AbFW as a percentage of eviscerated weight (AbFP). Among them, one SNP (carp089419) affecting both AbFW and AbFP reached the genome-wide significance level. Ten of those loci were harbored in or near known genes. Furthermore, relative expressions of 5 genes related to MFdo were compared using dorsal muscle samples with high and low phenotypic values. The results showed that 4 genes were differentially expressed between the high and low phenotypic groups. These genes are, therefore, prospective candidate genes for muscle fat content: ankyrin repeat domain 10a (ankrd10a), tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2 (tanc2), and four jointed box 1 (fjx1) and choline kinase alpha (chka). These results offer valuable insights into the complex genetic basis of fat metabolism and deposition.

Mapping QTLs of caudal fin length in common carp (Cyprinus carpio L.)

Common carp (Cyprinus carpio L.) exhibits significant morphological variability in the shape and size of the caudal fin. In this study, we used 190 progeny from two F1 parents to identify and map quantitative trait loci (QTLs) that influence caudal fin length (CFL) and the ratio (RCS) between caudal fin length and standard length (SL) based on a microsatellite genetic map of common carp. A total of 15 QTLs were detected in seven different linkage groups. One significant and eight suggestive QTLs affecting CFL were identified on LG8, LG14, LG29, LG32 and LG44, which explained 8.0%–22.1% of the phenotypic variation; six suggestive QTLs affecting RCS were detected on LG8, LG32, LG46 and LG48, which explained 7.0%–15.4% of the phenotypic variation. The QTLs for caudal fin length detected in this study may serve as a starting point for identification of genes involved in caudal fin development in common carp.

The complete mitochondrial genome sequence of Hemiculter leucisculus

Abstract The complete mitochondrial genome of Hemiculter leucisculus was determined to be 16,617 bp. It contains the structure of 22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNA genes, and non-coding control region (D-loop). The critical central conserved sequences (CSB-D, CSB-E, and CSB-F) were also detected. The determination of H. leucisculus mitogenome would play an important role in genetic diversity and population vitality in Cyprinidae.

Complete mitochondrial genome sequence of Romanogobio tenuicorpus (Amur whitefin gudgeon)

Abstract Amur whitefin gudgeon (Romanogobio tenuicorpus) belongs to the family Cyprinidae, it is freshwater aquaculture species in China. In the report, we determined the complete mitochondrial genome sequence of Romanogobio tenuicorpus, which is 16,600 bp long circular molecule with 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region, the conserved sequence blocks, CSB1, CSB2 and CSB3 were also detected.

Quantitative trait locus analysis of standard length, body depth and body thickness in mirror carp ( Cyprinus carpio L.): Quantitative trait locus analysis of standard length, body depth and body thickness in mirror carp ( Cyprinus carpio L.)

以镜鲤全同胞家系为材料,用246个SSR和306个SNP标记构建了鲤鱼的连锁图谱,利用GridQTL软件对体长（SL）、体高（H）、体厚（BT）和体长/体高（SLH）进行了QTL定位分析。结果显示：共检测到14个相关的QTL,分布在7个连锁群上。其中,7个与体长相关的QTL——LG6、LG17、LG21、LG23和LG35连锁群上的QTL为显著水平（P〈0.05）,LG1和LG28上达到极显著水平（P〈0.01）,可解释表型变异为6.6%~12.6%;3个与体高相关的QTL均为极显著水平（P〈0.01）位于LG17、LG23和LG28上,可解释表型变异分别为11.6%、12.7%和15.6%;2个与体厚相关的QTL均为显著水平（P〈0.05）位于LG23和LG28上,可解释表型变异分别为8.6%和7.2%;2个与体长/体高相关的QTL均为显著水平（P〈0.05）位于LG21和LG35上,可解释表型变异均为8.2%。Based on a full-sib family, the genetic linkage map was constructed with 246 microsatellite and 306 SNP markers, which was used to detect the QTLs for standard length (SL), body depth (H), body thickness (BT), and the ratio of standard length and body depth (SLH) in mirror carp by GridQTL software. The results indicated that a total of 14 related QTLs distributed on the 7 linkage groups were obtained. Seven QTLs were related to standard length, of which the linkage groups of LG6, LG17, LG21, LG23, and LG35 were at 5% significant level, and linkage group LG1 and LG28 were at 1% significant level, which explained 6.6%-12.6% of the phenotypic variance. Three QTLs were identified for body depth on the linkage groups of LG17, LG23 and LG28 (P amp; 0.01), accounting for 11.6%, 12.7%, and 15.6% of the phenotypic variance, respectively. Two QTLs were associated with body thickness on the linkage of LG23 and LG28 (P amp; 0.05), which explained 8.6% and 7.2% of the phenotypic variation, respectively. Two QTLs were responsible for the ratio of standard length and body depth on the linkage of LG21 and LG35 (P amp; 0.05), both of which explained 8.2% of the phenotypic variance. The results provide a useful reference for further candidate gene research and molecular marker assisted selection in mirror carp.

Quantitative trait loci for morphometric traits in multiple families of common carp (Cyprinus carpio)

Quantitative trait locus (QTL) mapping is frequently used to understand the genetic architecture of quantitative traits. Herein, we performed a genome scan for QTL affecting the morphometric characters in eight full-sib families containing 522 individuals using different statistical methods (Sib-pair and half-sib model). A total of 194 QTLs were detected in 25 different regions on 10 linkage groups (LGs). Among them, 37 QTLs on five LGs (eight, 13, 24, 40 and 45) were significant (5% genome-wide level), while the remaining 40 (1% chromosome-wide level) and 117 (5% chromosome-wide level) indicated suggestive effect on those traits. Heritabilities for most morphometric traits were moderate to high, ranging from 0.21 to 0.66, with generally strong phenotypic and genetic correlations between the traits. A large number of QTLs for morphometric traits were co-located, consistent with their high correlations, and may reflect pleiotropic effect on the same genes. Biological pathways were mapped for possible candidate genes on QTL regions. One significantly enriched pathway was identified on LG45, which had a P-value of 0.04 and corresponded to the “regulation of actin cytoskeleton pathway”. The results are expected to be useful in marker-assisted selection (MAS) and provide valuable information for the study of gene pathway for morphometric and growth traits of the common carp.